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<li><a href="./">Snakemake book</a></li>

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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Prerequisites</a></li>
<li class="chapter" data-level="2" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i><b>2</b> Introduction</a><ul>
<li class="chapter" data-level="2.1" data-path="introduction.html"><a href="introduction.html#ratinale"><i class="fa fa-check"></i><b>2.1</b> Ratinale</a><ul>
<li class="chapter" data-level="2.1.1" data-path="introduction.html"><a href="introduction.html#what-is-reproducibility"><i class="fa fa-check"></i><b>2.1.1</b> what is reproducibility?</a></li>
<li class="chapter" data-level="2.1.2" data-path="introduction.html"><a href="introduction.html#what-is-reproducibility-really"><i class="fa fa-check"></i><b>2.1.2</b> what is reproducibility, really?</a></li>
<li class="chapter" data-level="2.1.3" data-path="introduction.html"><a href="introduction.html#why-snakemake"><i class="fa fa-check"></i><b>2.1.3</b> Why Snakemake?</a></li>
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<li class="chapter" data-level="2.2" data-path="introduction.html"><a href="introduction.html#installation"><i class="fa fa-check"></i><b>2.2</b> Installation</a><ul>
<li class="chapter" data-level="2.2.1" data-path="introduction.html"><a href="introduction.html#recommended-way-to-install-snakemake"><i class="fa fa-check"></i><b>2.2.1</b> Recommended way to install <code>snakemake</code></a></li>
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<li class="chapter" data-level="2.3" data-path="introduction.html"><a href="introduction.html#install-software-using-conda"><i class="fa fa-check"></i><b>2.3</b> Install software using <code>conda</code></a></li>
<li class="chapter" data-level="2.4" data-path="introduction.html"><a href="introduction.html#backup-a-environment"><i class="fa fa-check"></i><b>2.4</b> Backup a environment</a></li>
<li class="chapter" data-level="2.5" data-path="introduction.html"><a href="introduction.html#whats-it-look-like"><i class="fa fa-check"></i><b>2.5</b> What’s it look like?</a></li>
<li class="chapter" data-level="2.6" data-path="introduction.html"><a href="introduction.html#how-do-we-use-it"><i class="fa fa-check"></i><b>2.6</b> How do we use it?</a></li>
<li class="chapter" data-level="2.7" data-path="introduction.html"><a href="introduction.html#what-does-the-worflow-look-like"><i class="fa fa-check"></i><b>2.7</b> What does the worflow look like?</a></li>
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<li class="chapter" data-level="3" data-path="literature.html"><a href="literature.html"><i class="fa fa-check"></i><b>3</b> Literature</a></li>
<li class="chapter" data-level="4" data-path="methods.html"><a href="methods.html"><i class="fa fa-check"></i><b>4</b> Methods</a></li>
<li class="chapter" data-level="5" data-path="applications.html"><a href="applications.html"><i class="fa fa-check"></i><b>5</b> Applications</a><ul>
<li class="chapter" data-level="5.1" data-path="applications.html"><a href="applications.html#example-one"><i class="fa fa-check"></i><b>5.1</b> Example one</a></li>
<li class="chapter" data-level="5.2" data-path="applications.html"><a href="applications.html#example-two"><i class="fa fa-check"></i><b>5.2</b> Example two</a></li>
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<li class="chapter" data-level="6" data-path="final-words.html"><a href="final-words.html"><i class="fa fa-check"></i><b>6</b> Final Words</a></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
<li class="chapter" data-level="7" data-path="paired-samples-for-snakemake.html"><a href="paired-samples-for-snakemake.html"><i class="fa fa-check"></i><b>7</b> Paired samples for snakemake</a><ul>
<li class="chapter" data-level="7.1" data-path="paired-samples-for-snakemake.html"><a href="paired-samples-for-snakemake.html#convert-dictionary-content-to-wildcards"><i class="fa fa-check"></i><b>7.1</b> Convert dictionary content to <code>wildcards</code></a></li>
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<li class="chapter" data-level="8" data-path="example.html"><a href="example.html"><i class="fa fa-check"></i><b>8</b> Example</a><ul>
<li class="chapter" data-level="8.1" data-path="example.html"><a href="example.html#example-snakemake-pipeline"><i class="fa fa-check"></i><b>8.1</b> Example Snakemake pipeline</a></li>
<li class="chapter" data-level="8.2" data-path="example.html"><a href="example.html#section"><i class="fa fa-check"></i><b>8.2</b> </a></li>
<li class="chapter" data-level="8.3" data-path="example.html"><a href="example.html#pe-and-se-reads"><i class="fa fa-check"></i><b>8.3</b> PE and SE reads</a></li>
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<li class="chapter" data-level="9" data-path="workflow-of-wgbs-data-analysis.html"><a href="workflow-of-wgbs-data-analysis.html"><i class="fa fa-check"></i><b>9</b> Workflow of WGBS data analysis</a></li>
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<h1><span class="header-section-number">Chapter 6</span> Final Words</h1>
<p>We have finished a nice book.</p>

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